SGI Acquires OpenFoam

OpenFoam is probably the most mature open source CFD tool available. There are plenty of niche CFD projects on SourceForge, but none that have really been able to generate the user/developer community that OpenFoam has. OpenFoam recently made the news because SGI "purchased" it for an undisclosed amount.

"Computational fluid dynamics (CFD) is one of the most important application areas for technical computing," said SGI CEO Mark J. Barrenechea. "With the acquisition of OpenCFD Ltd., SGI will be able to provide our customers the market's first fully integrated CFD solution, where all the hardware and software work together."

Basically, they hired all of the developers:

The entire OpenCFD team, led by Henry Weller, has joined SGI as full-time employees and will be based out of SGI's EMEA Headquarters located in the UK. SGI Acquires Maker of Open Source CFD Software

They also created the OpenFoam Foundation to ensure the continued development of OpenFoam under a GPL license. This is a very good thing for the development of OpenFoam to really take off. The foundation means that a true commons can develop around the software. SGI is clearly using OpenFoam as widget frosting, and they are selling support. This means their incentives line up with making the open version as good as it can be rather than crippling it in deference to a paid "pro" version. Good news for open source computational fluid dynamics.

Second HTV-2 Flight Test

The second HTV-2 test flight experienced a loss of telemetry about 9 minutes into the flight, very similar to the first test-flight. The post-flight analysis from the first flight indicated that inertia coupling caused the vehicle to depart stable flight (which lead the autopilot to terminate the flight). Here’s a relevant snippet from Bifurcation Analysis for the Inertial Coupling Problem of a Reentry Vehicle,

Inertial coupling has been known since around 1948 [1]. It is essentially a gyroscopic effect, occurring in high roll-rate maneuvers of modern high-speed airplanes including spinning missiles designed in such a way that most of their masses are concentrated in the fuselage. For such an airplane, a slight deviation of its control surface angle from the steady-state angle may lead to a drastic change in roll-rate, causing damage on its empennage; known as the jump phenomenon. Nonlinear analyses to elucidate this problem have been reported in [2, 3], for example. However, the airplanes treated in these works are stable around the equilibrium point of level flight. On the other hand, an intrinsically unstable reentry vehicle, if combined with a malfunction of its AFCSs, may result in a catastrophe once it falls into a high roll-rate motion.

This does sound an awful lot like what happened to both of DARPA’s HTV-2 vehicles. Departure from controlled flight due to inertia coupling was the cause of a loss of crew in the early X-2 testing [4].

Simple explanations are usually not the reason for flight test accidents or mishaps. Experience has shown that there is usually a chain of events that lead to the mishap. Day gives a great summary of the combination of contributing factors that lead to the fatal X-2 test [4],

• Optimum energy boost trajectory.
• The rocket burn was longer than predicted by 15 sec and positioned the pilot further from Muroc Dry Lake than expected.
• Decrease in directional stability as speed increased.
• Decrease in directional stability with increased lift, leading to a reduced critical roll rate for inertial coupling.
• Adverse aileron control (control reversal).
• High positive effective dihedral.
• Rudder locked supersonically.
• Mass properties in window of susceptibility for inertial roll coupling.

Day describes the result of hitting an unstable region in the control parameter space:

At critical roll velocity, violent uncontrollable motions characteristic of inertial roll coupling occurred about all three axes.

At low-speeds this might be recoverable, but it is simply intractable to design a hypersonic aircraft to handle the loads this kind of rapid motion imposes on the vehicle structure. Eventually something gives, and this “jump” leads rapidly to catastrophic failure.

Day summarizes the reasoning for not modifying the X-2 for manned hypersonic flight,

The X-2 was unfortunately in the twilight zone of progress where rocket power, structural integrity, and thermodynamics were sufficiently advanced to push the aircraft to supersonic speeds. However, hydraulic controls and computerized control augmentation systems were not yet developed enough to contend with the instabilities.

And a relevant snippet from the more recent bifurcation analysis,

If it has unstable dynamics in the neighborhood of a trim point, a slight external disturbance or a slight deviation of control surface angles from their precise values at the trim point cannot allow the vehicle to stay at the trim point [5].

The flight regime that HTV-2 is operating in is unknown enough that it is difficult for designers to know before flight if the flight profile will put the vehicle into an unstable region of the control space. I thought the language that the program manager (a fellow AFIT alum btw) used to describe the post-flight analysis was interesting,

“Assumptions about Mach 20 hypersonic flight were made from physics-based computational models and simulations, wind tunnel testing, and data collected from HTV-2s first test flight the first real data available in this flight regime at Mach 20,” said Air Force Maj. Chris Schulz, HTV-2 program manager who holds a doctorate in aerospace engineering. “Its time to conduct another flight test to validate our assumptions and gain further insight into extremely high Mach regimes that we cannot fully replicate on the ground.” DARPA Press Release

I've noticed physics-based is a common meme for climate policy alarmists trying to shore-up the credibility of simulation predictions. There’s that same tone of, “The Science Says...”, which leads to unwarranted confidence in a situation of profound ignorance (unquantifiable uncertainty). I’ve also observed that program managers seem to take great comfort in the aura of a model that is “physics-based” as a talisman against criticism (“just look at these colorful fluid dynamics, you must be really stupid to question Physics…”). Of course, “physics-based” can be said of all sorts of models of varying fidelity. It is a vague enough moniker to be of great political or rhetorical use. Not that I think Schulz is one of these shady operatives since he goes on to say,

“we wouldn't know exactly what to expect based solely on the snapshots provided in ground testing. Only flight testing reveals the harsh and uncertain reality.”

As DARPA has been well informed by recent experience, ignorance becomes apparent only when confronted with the reality of interest. “Physics-based” is no guarantee of predictive capability.

References

[1]   Abzug, M.J. and Larrabee, E.E., Airplane Stability and Control. A History of the Technologies that Made Aviation Possible, Cambridge University Press, Cambridge, U.K., Chap. 8, 1997.

[2]   Schy, A.A. and Hannah, M.E., “Prediction of jump phenomena in rolling coupled maneuvers of airplanes,” Journal of Aircraft, Vol. 14, pp. 375–382, April 1977.

[3]   Carrol, J.V. and Mehra, R.D., “Bifurcation analysis of nonlinear aircraft dynamics,” Journal of Guidance, Control and Dynamics, Vol. 5, No. 5, pp. 529–536, 1982.

[4]   Day, R.E., Coupling Dynamics in Aircraft: A Historical Perspective, NASA Special Publication 532, 1997.

[5]   Goto, N. and Kawakita, T., Advances in Dynamics and Control, CRC Press, Chap. 4, 2004.

Latex for Blogger: Pandoc

The previous post showed some new math rendering tools for supporting Latex for Blogger. That still relied on htlatex (in the tex4ht package) for converting Latex into HTML. I just found another tool called Pandoc that converts between lots of different markup languages. Here’s the first paragraph from the manpage.

Pandoc is a Haskell library for converting from one markup format to another, and a command-line tool that uses this library. It can read markdown and (subsets of) Textile, reStructuredText, HTML, and LaTeX; and it can write plain text, markdown, reStructuredText, HTML, LaTeX, ConTeXt, RTF, DocBook XML, OpenDocument XML, ODT, GNU Texinfo, Medi‐ aWiki markup, EPUB, Textile, groff man pages, Emacs Org-Mode, and Slidy or S5 HTML slide shows.

Sounds promising. So, this post is written in Latex, and then I converted it to HTML with this command:

  [jstults@grafton pandoc]$ pandoc -f latex -t html -o pandoc.html pandoc.tex 

Here’s some test equations:
f(x) = x²

$\frac{\partial U}{\partial t} = \nabla U $

Φ  = ϕ - ∫ _t0^tf(τ) dτ

Computational Explosive Astrophysics

I got an update with an interesting set of slides on adaptive mesh refinement recently. I've always been more of a moving mesh kind of guy, but lots of people find the AMR approach useful. The slides are for a summer course on Computational Explosive Astrophysics. They have an index for the lecture notes where those slides came from. Last year's course was Galaxy Simulations.

Latex for Blogger

A couple of years ago, I posted that I was using htlatex to do math-heavy posts. This worked in a pinch, the equations are all nicely rendered as *.png’s and they have all the normal Latex auto-numbering and cross-referencing. This only works for posts though, no equation support in comments. I learned about MathJax, which is a much better option than non-scaling pngs for math, and it supports equations in comments. All it requires is adding a script to the blogger template file.

  <script src=’http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML’ type=’text/javascript’> 
  </script>

Then run htlatex with the mathml option.

  [jstults@grafton]$ htlatex foo.tex ”xhtml,mathml”

This turns foo.tex into foo.html, which has the equations in MathML markup. MathJax renders the MathML so everything looks pretty.

MathJax also renders any Latex it finds on the page (including in comments!). The normal single dollar sign for inline math does not work, since this would cause trouble if people were trying to discuss money. Here's what does work though:

  % inline math in comments use: 
  $$ x + y = z $$ 
  % equations in comments use: 
  \[ x + y = z \] 
  % or  (for numbered equations): 
  \begin{equation} x + y = z \end{equation}

 inline in comments:  
 \ ( x + y = z  \)

A couple numbered equations in the post \begin{equation} \frac{\partial x}{\partial t} = A x \end{equation} foo \begin{equation}\frac{\partial y}{\partial t} = g(y) + f \end{equation}

Why ALPAL

Really it's "why use symbolic math programs to develop number crunching software," but these are from the doc_282 in the ALPAL docs (my emphasis).

• First, physics code could be generated and modified to incorporate new physics and features at a much greater speed than occurs with present codes. Such a language would directly foster improvements in the physics models employed, as well as teh numerical methods used to approximate these models. Two reasons point out the need to experiment with numerical methods for a given set of integro-differential equations. First, as a direct consequence of the paucity of mathematical theorems that constructively characterize partial differential equations (PDEs) in general, there is no means of determining what approximation technique will most faithfully capture the solution. Second, in almost all cases, analysis of an approximation technique is limited to idealized linear problems, so the stability and convergence properties of applying a given approximation technique to actual set of PDEs is unknown. Thus, the optimal algorithm for solving any given PDE or set of PDEs is not known, and any tool to aid the computational physicist must be capable of dealing with many different numerical algorithms and methods.
• Second, much of the drudgery and concomitant errors in constructing simulation codes would be eliminated by such a language. Large amounts of uninteresting algebra are associated with both the development of appropriate physical models and the discrete versions of the these models on a computer. If the algebraic work involved could be largely automated, computational physicists could spend a great deal more time doing the physics they were trained to do.
• Third, a more natural way of describing the physics model is possible with such a language. Errors in the modeling and numerical approximation process would become more obvious, thereby reducing the number of errors in the simulation code.
• Fourth, it becomes possible to automate the computation of Jacobian matrices both for linear and nonlinear problems. Not only would this automatic calculation greatly reduce the number of algebraic errors commited for those cases that solve linear systems of equations (with or without a nonlinear solver0, but it would make possible a large number of implicit techniques for situations where it has just not been feasible to use them in the past.
• Fifth, such a language could fulfill the need to optimize the very expensive computation that goes on in simulation codes. While a competent scientis can do a good job of optimizing a simple simulation code, the complexity of this task for large simulation codes is beyond the capabilities of even the most skilled scientist. Moreover, optimizing a code is a mundane task that once again does not reward the scientist in his primary pursuit. Optimization becomes an even more critical issue on non-scalar computer architectures such as the CRAY-XMP or an ultracomputer. A high-level view of how to vectorize and/or parallelize a given algorithm (or meta-algorithm) on one of these supercomputers is crucial so the scientist can substantially improve the cost-effectiveness of a simulation on that computer. In principle, a language like ALPAL can provide such a view.
• Sixth, since the cost of developing simulation codes is great, especially for new machine architectures, this language could be used to dramatically cut development costs. This is true whether a simulation code is being created for a new machine or whether it is being ported from a previously used computer. Experience with vector computers over the past decade at LLNL has taught this lesson well. More recently, some simulation codes have been ported to the CRAY-XMP, with use being made of its distributed computing capability. This porting to a distributed computer has required an even larger investment of manpower. These large manpower development costs will be repeated many times because a great variety of parallel computers are now appearing, and because parallel computing is a far greater technical challenge than even vector computing.
• Seventh, more complete and coherent documentation can be developed with such a language. In fact, a journal-style specification of a code can provide many details that are not generally provided in a journal article about the code. The journal-style specification is expressly designed for readability, wheras the text of a traditional simulation code is not. This is so because it is impossible to express high-level mathematical concepts such as derivatives and integrals together with their numerical approximations in Fortran or any other conventional high-level language.

International Journal for Uncertainty Quantification Latex Template

I had a bit of trouble getting the Latex document class, ij4uq.cls, for the new International Journal for Uncertainty Quantification to work on my install of Fedora 14, so I figured I'd share my recipe for making it work. The editor and journal support staff were very helpful with quick responses and useful pointers.

First you need to download IJ4UQ Latex Template and unzip that in a convenient location.

[jstults@grafton ij4uq]$ unzip IJ4UQ-Latex-Template.zip

This creates a directory with the ij4uq.cls file you need to make documents for the journal. Instead of the standard article class you'll have something like

\documentclass[review,article]{ij4uq}

at the top of the Latex document. The zip file also contains author instructions, a latex template document, a readme and instructions on installing the Palatino font which is required by the journal style.

The reason I had so much trouble getting this style to work is that Fedora still uses TexLive 2007. There is an effort underway to update things to TexLive 2010 for Fedora 15. Until that becomes standard, you have to turn on a development repository and install texlive. Unless you want to really break your distro and install the styles by hand. However, the sane way is to use the package management system as much as possible.

Second you need to turn on the development repo and update (or if you don't already have texlive installed, then install texlive).

[root@grafton ij4uq] rpm -i http://jnovy.fedorapeople.org/texlive/2010/packages.f14/texlive-release.noarch.rpm [root@grafton ij4uq] yum clean all && yum update

Warning: this is a fairly significant download. Be prepared to go do something else while this crunches.

Third, try to compile the template document. It will likely break because you don't have all of the required *.sty files. Since you are running the sweet new development version of texlive, you can specify these to yum as they apear in the Latex error messages. This saves you from needing to track down which Fedora package provides the particular style file you are missing. This one-liner should get you most of the way there.

[root@grafton ij4uq] yum install 'tex(arial.sty)' 'tex(sectsty.sty)' 'tex(appendix.sty)' 'tex(changebar.sty)' 'tex(nicefrac.sty)' 'tex(lineno.sty)' 'tex(overpic.sty)' 'tex(stfloats.sty)' 'tex(textfit.sty)'

Fourth, you need to fix the unfree floatflt.sty.

[root@grafton ij4uq] mkdir -p /usr/share/texmf-texlive/tex/latex/floatflt [root@grafton floatflt] cd /usr/share/texmf-texlive/tex/latex/floatflt [root@grafton floatflt] rm -f floatflt.* float*.tex [root@grafton floatflt] wget http://mirror.ctan.org/macros/latex/contrib/floatflt/floatflt.ins [root@grafton floatflt] wget http://mirror.ctan.org/macros/latex/contrib/floatflt/floatflt.dtx [root@grafton floatflt] latex floatflt.ins [root@grafton floatflt] texhash

Fifth, you need to update the font maps for the new fonts.

[root@grafton ij4uq] updmap-sys --enable Map /usr/share/texlive/texmf-dist/fonts/map/dvips/palatino/upl.map

That's it. Now the ij4uq.cls template document that comes with the zip file should compile on your (only slightly broken) Fedora 14.

Storms of Our Grandfathers

Are we "rolling 13s" and getting thousand year storms every year?

NOAA April 2011 Precipitation Anomaly

The contour plots below are taken from Theory of the hydraulic jump and backwater curves. These studies of historical storm records were used to inform design decisions for the Miami Valley Conservancy District's retarding basins and channel improvements following the 1913 floods. My previous post has pictures of the hydraulic jump below Huffman Dam in operation.

My question to Dr Curry about what value high-fidelity (read: relatively expensive to run and analyze) climate simulations have for decision makers was motivated by reading up on infrastructure projects like the retarding basins and channel improvements in the Miami Valley. I think it would be interesting to take a look at a historical project like this that included rudimentary analysis of climate (weather event frequency and magnitude) in its design, and say, "here's how it would be informed differently using modern tools."

The design philosophy taken by the engineers working for the Miami Valley Conservancy District was to design for the worst possible case (historical records from Europe were also considered since they went back further and more reliably) plus roughly twenty percent margin due to the inherent uncertainty in estimating the worst possible case.

If it were necessary to depend wholly on the records of storms which have occurred in the United States, it might be thought possible for moderately great storms to occur over a period of a few hundred years, and then to find, as an exception, a storm three or four times as great. Theoretically that is very improbable, simply because water vapor in sufficient quantities cannot be transported from the ocean or gulf fast and long enough to cause such exceptional storms. As stated in chapter XI, however, records were collected of the stages of rivers in Europe for long periods of time, and these furnish fairly conclusive proof that such great exceptional storms actually do not occur. On the Danube at Vienna, for instance, we have records since about the year 1000 A.D.; fairly accurate records are available for stages of floods in the Tiber at Rome for more than 2,000 years; and records have been made of floods on the Seine at Paris for a long period of years.
Relation of Great Storms to Maximum Possible

After making the extensive investigation of storms in the eastern United States, it is believed that the March, 1913, flood is one of the great floods of centuries in the Miami Valley. In the course of three or four hundred years, however, a flood 15 or 20 per cent greater may occur. We do not believe a flood will ever occur which is more than 20 or 25 per cent in excess of that of March 1913. There is a factor of ignorance, however, against which we must provide, and the only way to do this is arbitrarily to increase the size of the maximum flood to be provided for. If longer records were available a closer estimate could be made, but in planning works on which the protection of the Miami Valley depends, it is necessary to go beyond human judgment. This has been done on all the other phases of the design, and we believe it would not be good engineering practice to stop at our judgment on this phase. We must be able to say that the engineering works are absolutely safe in every respect. For this reason provision is made for a flood nearly 40 per cent greater than that of March 1913. This is 15 or 20 per cent in excess of what is believed to be the greatest possible flood that will ever occur.
Reasons for Choosing as a Basis for Design a Flood 40% Greater than that of March 1913

Would modern tools cut the design margin due to reduced uncertainty or would they indicate that the project is now under-designed due to projected climate change? The latter seems unlikely considering that the magnitude of the purported effects has been repeatably shown to be smaller than we can reliably detect given the length of our data record. Would there be any practically significant changes to the decisions and designs? If your system already has sufficient margin for projected changes in weather-event magnitude do projected changes in frequency matter?

Technocrats and Philosopher Kings can Save our Impotent Polity

Wow, really awesome article on Climate Resistance, Trust Me, I Speak for Science. I liked these parts from the concluding paragraphs especially. I think you'll notice the parallels to my posts, The Social Ethic and Appeals for Technocracy and No Fluid Dynamicist Kings in Flight-Test.

This metaphysical confusion runs throughout Mooney’s argument. For Mooney, ‘ideology’ is some insidious, toxic force, the antithesis to ‘truth’ itself. The thrust of his argument is that we need particular scientific institutions to ameliorate this intrinsic weakness of human nature. And as such, these institutions deserve elevated status above the reach of those prone to ideology. Otherwise, we would tend towards creationism, to MMR-scares, to climate-change denial. In other words, our flawed minds would create a catastrophe, and it is this possibility of catastrophe that seemingly legitimises the elevated position of scientific institutions. Mooney reinvents Plato’s city state administrated by Philosopher Kings, the main differences being that Mooney conceives of a global polity, and the wisdom of the Guardians only produces the possibility of mere survival, not even a better way of life. To bring this back the matter of trust, Mooney doesn’t trust humans. Their minds are flawed. Their ambitions and ideas are mere fictions. The institutions they create are accordingly founded on false premises, which, instituted and acted upon, will cause disaster. Even when humans are exposed to ‘the truth’, it is, on Mooney’s view, absorbed into the poisonous, ideological programmes of partisans: liars and cheats who distort it. But without a disaster looming, this instance of a politics of fear would collapse.

He simply can’t make a popular argument for his political idea, and so turns to ‘science’ to identify the necessity of such a programme — i.e. the crisis — and to identify reasons why conventional democratic processes cannot realise it...

It's always a good day when you can throw a little Plato into the mix ; - )